I haven't noticed much of a difference. But to the extent we've seen him get beat more off the dribble, I think that's just b/c who he's being asked to defend. Matt Jones is a very solid defender who does a good job against bigger bodied guards and wings. However, he lacks the lateral footspeed to stay in front of very quick guards who are good off the dribble.
Last year, Matt was rarely, if ever, asked to guard PGs and quick SGs b/c Quinn Cook and Tyus Jones were assigned those responsibilities. This year, by contrast, Matt is often being asked to defend the opponent's PG whenever Thornton is not in the game -- as Jones is a better on ball defender than Allen and Kennard + Allen is too valuable on offense to risk getting him in foul trouble trying to stay in front of other team's principal ballhandler. IMO, if anything, Matt's just a victim of the matchups we're giving him whenever Thornton's not on the court.
Also, it doesn't help that Matt's offense has been pretty abysmal. While obviously he's hardly to blame in the Clemson - Syracuse stretch, Matt missed a few big late game shots that I think are messing with his confidence.